Fig. 3

P53 pathway was up-regulated after RG7388 treatment. A Hierarchical clustering of significantly changed genes (adjusted P-values < 0.05, fold change > 1.5) of HSJD-DIPG-007-NTC and HSJD-DIPG-007-TP53 KO lines after treatment with DMSO and RG7388. Columns in the heat map represent individual replicates (three for each condition). Rows represent genes, colored by log-transformed transcript intensity (DESeq2-normalized counts + 1) in z-score. Blue shows replicates with low expression (z-score < 0); red shows replicates with high expression (z-score > 0). B Top five most differentially regulated KEGG pathways of HSJD-DIPG-007-NTC and HSJD-DIPG-007-TP53 KO lines response to RG7388. C Hierarchical clustering of significantly changed genes (adjusted P-values < 0.05, fold change > 1.5) within the p53 pathway of HSJD-DIPG-007-NTC response to RG7388. Columns in the heat map represent individual replicates (three for each condition). Rows represent genes, colored by log-transformed transcript intensity (DESeq2-normalized counts + 1) in z-score. Blue shows replicates with low expression (z-score < 0); red shows replicates with high expression (z-score > 0). Volcano plot of p53 pathway genes with significant change (adjusted P-values < 0.05, fold change > 1.5). Blue, red and gray show down-regulated, up-regulated and not significantly changed genes, respectively. D Protein expression level of MDM2, p53 and p21 in HSJD-DIPG-007-NTC and HSJD-DIPG-007-TP53 KO treated with DMSO or 25 nM RG7388 for 6 h, 12 h, 24 h and 48 h. E Protein expression level of MDM2, p53 and p21 in five TP53 wild-type (Top) and five TP53 mutant (Bottom) DIPG cell lines treated with DMSO and 100 nM RG7388 for 24 h